Apex The Biggest Daddy
by KyuubiKitsune9
Summary: Naruto was kidnapped from the Elemental Nations when he was just a baby. He now travels through a city hidden underwater for a purpose. What that purpose is even he doesn't know. Grey! Naruto, Strong! Naruto, Harem with Big Sisters and Little Sisters that grow up to love him. Rated M for Gore, Profanity, Lemons. Some things are changed in the Bioshock Universe.
1. Chapter 1 The Beginning

**A/N: Alright all here's a new story for ya! If you're one of the readers from The Sins Summoner and you're wondering why I put it on Hiatus, it is because I have grown slightly bored of the story so I'm taking a break from it so that I don't abandon it. This is just a story that I will update whenever I want/can if I want to and it's one of the subjects I've been thinking over and building on over a few days.**

**For this story I won't be putting Authors Note's unless their absolutely needed and I will only say this once, I DO NOT OWN NARUTO OR ANY OF THE BIOSHOCK SERIES, THEY BELONG TO RICH PEOPLE THAT LIVE SOMEWHERE ON THIS GREEN AND BLUE EARTH!**

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**The Beginning**

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One day in the elemental nations there was a big attack on a large ninja village called Konohagakure. Their 4th Hokage had a child with his hidden wife on the same day of the attack. The attack was caused by one of the nine great bijuu that inhabited the earth, the strongest of the nine, the Kyuubi no Kitsune. The 4th Hokage had sealed the beast in all of its entirety inside of his son while on his and his wife's deathbed. Their last and dying words were the boy's name, Naruto Uzumaki. The seal did not allow the boy to inherit or use any of the beast's chakra but in turn the boy gained the beast's unholy healing capability. When the boy was just 1 and 3 months old he was kidnapped from the orphanage he resided inside of. No-one had known he was kidnapped until it was too late, and the people celebrated. The kidnappers had taken the boy out deep into uncharted parts of the ocean, land neither visible nor available for thousands of miles. Atop of that ocean stood a large cement tower that had a golden statue of an angel that was reaching for the sky. The boy's kidnappers took him inside and what it had inside of it was a large metal sphere that was floating atop the water. They took the boy inside the sphere and headed downwards. Once they finally left the darkness after 30 minutes they were greeted to the site of large underwater skyscrapers. Just before they entered the Toddlers Orphanage, they were greeted with a sign that said 'Welcome to Rapture!' They exited the sphere and were greeted with the site of their employer, leader, and creator of the fine city. Andrew Ryan. He stood their imposingly, before ordering them to send the boy to the cribs.

Over the course of 17 years they experimented on the boy, intent on creating a better version of a Big Daddy, for the current alpha type were not enough. Once the boy was of the ripe age of 8 they started _injecting_ him with all kinds of vials. The first that they injected into the boy was a plasmid that would make him obey every order that Andrew gave. It was a great success and thus they injected the next plasmid which would cloud and lock off anything personal that wasn't fatal on his mind, killing his emotions besides 2 and his own thoughts, robbing him of his personality, the only things inside of his mind were 3 things. To follow Andrews orders without question, To protect every little sister in site, and To go berserk in case anyone got near him or the Little Sisters that weren't Big Daddies. Andrew tried to bond the boy to a little sister but to his and everyone else's surprise he couldn't bond with any of them, though he would be _very_ protective of any in his sight. They then started experimenting with Gene Tonics on the boy. They injected him with a combination of muscle enhancers that would bulk him up and make him undeniably strong. To their surprise the boy's body did not reject the tonic at all; in fact it had readily accepted the tonic, as if it was _welcoming_ it. Even furthering their surprise was that instead of bulking him up with Red Muscle like it was supposed to, he instead gained Pink Muscle. It kept the boy skinny and flexible for speed and attacking attributes while making him incredibly strong to up his strength.

They immediately got to work on this new subject, hoping to make him more powerful than before and for him to become their ultimate weapon. They first tried experimenting with ADAM slugs. They first started with an empty ADAM slug that was white and pale that generated its own ADAM at a very slow pace. They injected the slug into his stomach and thinking that the boy would go into a cardiac arrest or shock to their _once again_ surprise the boy's body _absorbed_ the slug. They tested him to see what had happened and to their shock the boy's body had started generating its own ADAM, albeit very slowly. So they once again tried to inject him with another ADAM slug that was harvested from one of the successful Little Sister experiments. His body once again absorbed the slug except this time his body started generating ADAM at a much more rapid pace. So they got to work with the public plasmids.

They first injected him with the Electricity plasmid that would allow the boy to control Electricity from his hands. The boy's body readily accepted the plasmid and no problems occurred, and he was able to use the Electricity as easy as breathing, when asked to describe what it was like for him, and they started injecting him with other plasmids. They first did the Incinerate plasmid that would allow him to control fire in the same way as the Electricity plasmid, his body once again accepted the plasmid with no problems, and he was able to control it to the _exact same_ degree as his Electricity plasmid. Once again he described it as easy as breathing when asked and they immediately got to work. They named him Project Apex and his name from then on was Apex. They then injected him with every other plasmid that was out in production, Scout, Telekinesis, Ice, Decoy, Security, Hypnosis, and Insect Swarm. He showed no problems in accepting these plasmids and they were pleased to see that he was able to use them to the same degree as his Electricity and Incinerate plasmids. They then injected him with the four experimental plasmids that they had, the other Big Daddies were not so accepting with the plasmids and immediately would die in a multitude of gruesome ways, though some regular's that used the plasmids that were starting to be known as Splicers were able to accept them though each splicer that used any plasmids that were gained had horrible growths and other things appear on their body, the most noticeable being that their faces were horribly disfigured and they started craving ADAM like maniacs.

The first experimental plasmid they injected him with was the Teleport plasmid. His body accepted it readily and he was able to use it with no problems except for the disorientation that came from using it the first few times, they noted that instead of the regular cloud of red that the Houdini Splicers, as they started calling them, had and instead his was pitch black though he still had the audible pop and sucking sound as the Houdini Splicers. The next experimental plasmid that they injected into him was the Acid plasmid that would allow him to spew acid from his hands at will. His body accepted this with a little more difficulty than with the other plasmids as his body started melting on the inside but, as they had started to expect, his bodies insides had started healing themselves at a rapid rate and the acid was immediately dispelled from his body and he was able to use it with no problems. The third experimental plasmid they injected into him was the Wind plasmid, their other experiments with the plasmid would cause them to explode in a large and gory way that often left the scientists and Andrew covered in blood, limbs, flesh, organ-brain-bone matter, and muscle tissue.

Though with Naruto he was able to use the plasmid and throw gusts from his hand that could blow a hole in the wall with ease. Andrew and his scientists were happy with how Project Apex was going and with how the city was starting to crumble and how nearly 90% of the city was splicers of every kind they were glad they would have the ultimate protector. The final experimental plasmid was the Poison plasmid. This plasmid allowed him to throw all kinds of poisons from his hands that's effects would change as he wished. His body once again accepted the plasmid with no problems.

After all these experiments were done Naruto was just 13 years old. They started making a suit for him that wasn't as bulky and large as the other Big Daddies. His was skinny, almost skin tight, and allowed him to move and bend as he pleased. His helmet was that of a large round one that had glass portholes on the front, left, and right sides. He had a large container for ADAM with a needle and pressure control strapped to his right arm, so that he could gather ADAM for the scientists and Andrew if they so wished him to. They changed his voice into the deep, guttural voice that the other Big Daddies had. Naruto discovered that he still had the ability to speak but seeing as he hadn't spoken since they started the experiments he decided against telling Andrew and the scientists. Andrew and the scientists pit him against every type of Big Daddy that they had and to their surprise and glee he was able to dispatch them with ease, jumping from walls and the roof with ease distracting them using his plasmids abilities before stabbing them with his needle and draining their ADAM, killing them. They had truly created their ultimate weapon.

Though that isn't to say they didn't have any problems. For example, when they had tried giving the boy a Drill instead of the Needle they saw he struggled to use it, though they were in the process of trying to bond him once again to a little sister. Professor Suchong, a Little Sister, and Apex were gathered in a room and the Little Sister had kept asking her 'Grandpa Suchong' to play with her. Suchong eventually snapped and slapped the little girl. Apex immediately reacted and tackled Suchong onto the desk and impaled him with Apex's temporary Drill. His body is still there as no one wanted to remove it so it would serve as a reminder to always be careful around Apex.

Once the boy had turned 16 they gave him his customary suit, built in oxygen generator and needle in all, and sent him out. They had found that the boy had stopped growing once he reached the tall height of 6"3' and saw that it was because of his internal ADAM generator and the plasmids and Gene Tonics inside of his body that stopped his growing process. After he received his suit he also gained his final 3 orders, and they released him into Rapture. Though Andrew Ryan, Frank Fontaine, Brigid Tenenbaum, and Sofia Lamb all had reservations about releasing him. Andrew because he was wary about losing his ultimate protector and the fact that Apex did not have a Little Sister to bond with. Frank because he had also lost his possible ultimate protector and gatherer as well. Brigid because she had started regretting doing all these experiments with the Little Sisters and of what she did to Apex, shortly after he was released and far away enough she retaliated against Andrew and fled, taking a small amount of Little Sisters with her so that she may right this wrong that she had created. Sofia Lamb because she had wanted to use him to protect her daughter Eleanor Lamb, that would be born in a few months, from others. She got the original idea of Big Sisters from Apex and had holed herself up in the Persephone district and got to work. After 5 months her daughter was born and the Big Sisters were complete.

Apex is now 17 years old, though he doesn't know that, and travels the halls of Rapture with no real goal other than protecting any little sisters along the way if they and their Big Daddy were being attacked. Following Andrew Ryan's final 3 orders to the letter.

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**A/N: Alright so here's the first chapter, hope you guys enjoyed and just so you know, this will be a Harem story with Naruto, a few Big Sister's that I will give personality to, and, though Apex/Naruto doesn't know it, Little Sisters that will eventually grow up and love him. SLIGHT SPOILER TO THE STORY Naruto will eventually escape to the surface and back to Konohagakure with the people he will take with him but that's all I'm tell you guys about the future of this story.**


	2. Chapter 2 The Start

**The Start**

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Apex was currently travelling through Olympus Heights, meandering on through the halls not knowing where he was going but knowing where he's been. Strangely ever since he had entered Olympus Heights he noticed that there was a dramatic drop of Splicers and Big Daddies, like they were avoiding this area but not at the same time. Over the last year when they had released him they would call him back every few days for more experiments, said experiments being additions to his suit. The first addition they added was a Monthly Daily Hourly Minute Second clock on the inside left part of his helmet. It was a simple flip clock that would click down numbers by using flaps with the numbers on them. They had also experimented using music, trying to see if music caused anything to happen to the Big Daddies and Apex. They learned that placing Classical calming music would calm down the Big Daddies but not Apex. Apex had a multitude of different reactions to music, though some songs lyrics would cause strange feelings inside of his chest but as quickly as they had arrived they would disappear. He started wondering why exactly he was doing anything for them and once again the thought left his mind as soon as it appeared, his eyes flashed red before going back to the calm yellow in irritation. Why couldn't he form his own thoughts! It frustrated him to no end but he eventually gave up on trying to make his own coherent thoughts, seeing as they would all leave immediately as they came.

His final 3 orders rang in his head repeatedly over and over. Protect all Little Sisters in sight, Listen to Andrew Ryan's and his scientist's orders without question, and finally Go berserk when a Little Sister is endangered. He was snapped out of his thoughts by a voice coming over the intercom, booming all around him and his surroundings.

"Herr Apex why are you here? Did Andrew send you?" A female voice sounded over the entirety of the railroad he was in, just now realizing he had made it to a train station. Apex shook his head no and waited for the voice to come back.

"That's good, I'm sorry for what I'm about to do to you Apex…" The voice said throughout the hall and Apex got on his guard, those were _not_ safe words. But as soon as he had gotten ready to fend off any threat he felt increasingly strong impacts on the back of his helmet. But the impacts had left as suddenly as they came, so he prepared himself better this time, having losing his guard when the voice ended because he didn't see any Splicers or Big Daddies around. He heard loud rumbling from above so he looked upward; the last thing he saw was a large collect of debris falling directly on top of him.

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Apex got up groggily, his vision swimming and his head banging loudly. He studied his surroundings and found he thankfully still had his suit on. Then when he had finished studying his surroundings, he was in a small dank room that had 2 beds on the back right and left walls and childish drawings across the walls, in walked one of the Scientist's whose orders he was supposed to follow without question. Brigid Tenenbaum.

"I see you are finally awake herr Apex. I have suctioned out the plasmid inside you that did not allow you to think properly and made you a lap dog for Andrew." Tenenbaum said and Apex immediately felt like something had imploded inside of his thoughts. He immediately noticed he couldn't remember one of his orders, he could only remember two of his final orders, To protect every Little Sister in sight, and to go berserk if one of them was endangered. Why couldn't he remember the third!

"I order you to forget every previous order you have received." Tenenbaum continued and Apex felt two more things implode inside of his head and he realized he couldn't remember his last two orders! Then his head had started throbbing painfully. Tenenbaum approached the bed he was on and started talking again.

"I am going to suck out the last plasmid that has your memories locked away; we administered it to you when you were just three years old so you wouldn't remember anything we did to you." Tenenbaum said before she stuck a needle into one of the small holes near his neck that's purpose was for plasmids to be injected. He didn't notice the needle until it had been too late and Tenenbaum pulled back with an EVE syringe that had a weird Purple and Green mixture inside. Apex's head had stopped hurting and he was relieved because the pain had left. Then just as that thought had formed, his head felt like it was exploding repeatedly. He grabbed his head in immense pain and he reacted with one of the two emotions he knew. _Rage_. He lashed out as Tenenbaum jumped backwards and he smashed the bed into two parts. He grabbed one end and chucked it at the right side wall and clutched his head again. He started being assaulted by every memory that was locked away coming back violently. He fell to his knees after a few minutes and everything had gone silent. Apex slowly got up and Tenenbaum noticed that the lights of his porthole turned red and she backed away.

"**ANDREW RYAAAAAAAAAANNNNNNNN!**" Apex yelled out in complete rage, his deep guttural baritone voice making it that much scarier. He undid his helmet and threw it to the ground in anger, revealing his exceedingly pale skin, black whisker marks and red eyes of anger. He still couldn't feel any emotions beside Calmness and complete Rage but right now he just wanted to tear Andrew limb by limb. He turned to Tenenbaum and started interrogating her angrily.

"You were one of the scientists' that did this to me! Why did you help me?!" Naruto shouted at her, a strange warm feeling in his chest that made him wish that she would tell him, not knowing what this was scared him before his rage shook that away.

"I helped you because I want to right my wronging's herr Apex. I will help you get revenge on Sofia and Andrew if you help me." Tenenbaum said as she noticed his eyes turning yellow before changing into an electrifying blue that entranced her slightly.

"What do you need help with…? I will help so long as I get revenge…" Apex said calmly staring her in the eyes.

"I want you to help me gather as many Little Sisters as you can and once you finish with your revenge on Andrew and Sofia then you, me, and any Little Sisters with us that we have rescued will leave immediately…" Tenenbaum replied as she got closer to Apex.

"Fine, I'll help as many as I can, I just want out of here and to get my revenge. But know this, I _will_ destroy this _fucking_ city, I want to destroy every single one of Andrew's creations, so that _no-one_ will remember him…" He said as he went silent, studying her for any signs of defiance.

"Agreed, now let's go, I'm sure the little ones would like to see their new protector." Tenenbaum said with a smile as Apex picked up his helmet and placed it back on his head, going back to his silent demeanor. They walked out of the small room and down a hallway that had scribbles littering the walls. They arrived at a large room that had what looked like 12 Little Sisters doing various things, from playing with toys to drawing on the walls.

"Girls, meet your new protector, he's going to help get your other sisters and bring the bad people to justice." Tenenbaum said trying to make him seem like their knight in shining armor.

"You look different than Daddy." One of the Little Sisters said as they crowded around Apex.

"It's because he's going to protect you and being big doesn't help." Tenenbaum replied as Apex headed towards a torn couch that was in the back of that large room. He sat down and the Little Sisters crowded around him, one even climbed onto his lap as he stared at them all curiously.

"What are you doing little ones?" Tenenbaum asked curiously.

"Mama Tenenbaum we want to hear a story or song from Daddy." One of them replied.

"I don't think he-"Tenenbaum was cut off by Naruto placing a hand up to halt her. He brought his hand up to his helmet and pressed a button that was just below the front facing porthole. Then soft music started to play and lyrics started.

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Come, little children, I'll take thee away

Into a land of enchantment

Come, little children, the time's come to play

Here in my garden of shadows

Follow, sweet children, I'll show thee the way

Through all the pain and the sorrows

Weep not, poor children, for life is this way

Murdering beauty and passions

Hush now, dear children, it must be this way

Too weary of life and deceptions

Rest now, my children, for soon we'll away

Into the calm and the quiet

Come, little children, I'll take thee away

Into a land of enchantment

Come, little children, the time's come to play

Here in my garden of shadows

After the song had ended the Little Sisters and Apex were asleep, evidenced by the calm heaving of his chest. Another voice cut through the silence before the song faded away.

"Song: Children of the Night." The voice said before the recording stopped entirely. Tenenbaum looked onwards to the small gathering of sleeping Little Sisters before she headed towards her private room, letting them sleep for a while, not knowing how long Apex has gone without it.

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**A/N: Alright finished, now the reason these first two chapters were so short is because they are Prologue chapters. Meaning that these were just to show what had happened to reach the present point. The next chapter starts a few months after this incident. The chapters after the first two will be longer so don't worry about that. Also don't worry about music becoming a common thing in this story, this chapter will be the only one from now on with lyrics in it.**


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